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RSEM Specifications

Process Details

  • Name: RSEM
  • Process UUID: 20bdc2aa-ed05-11e8-9ce4-85221b21564c
  • Process Group: Transcript Quant.

Overview

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. This process quantifies transcript abundance by probabilistically assigning reads to transcripts, providing accurate estimates of both gene-level and isoform-level expression from paired-end or single-end RNA sequencing data.

This process is implemented in Bash, which invokes RSEM for transcript quantification and samtools for BAM file processing.

Key Functionality

  • Transcript Quantification: Estimates gene and isoform expression levels using probabilistic read assignment
  • Multiple Alignment Methods: Supports STAR, Bowtie, and Bowtie2 alignment backends for flexible read mapping
  • BAM Output Generation: Produces genome-coordinate BAM files with posterior probability annotations
  • Strand-Specific Analysis: Optional sense/antisense quantification for strand-specific protocols

Input/Output Specification

Inputs

Required Inputs

  • Mate Configuration

    • Description: Sequencing library type specification (single-end or paired-end)
    • Format: mate

  • RNA-Seq Reads

    • Description: Raw sequencing reads in FASTQ format
    • Format: fastq

  • RSEM Index

    • Description: Pre-built RSEM reference index for transcript quantification
    • Format: rsemIndex

Outputs

  • RSEM Quantification Results

    • Description: Gene and isoform expression estimates with statistical measures
    • Format: rsemOut

  • Alignment BAM Files

    • Description: Sorted BAM files with read alignments mapped to genomic coordinates
    • Format: bam

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • RSEM Reference Type

    • Description: Alignment method for read mapping
    • Available options: star (default), bowtie, bowtie2

  • RSEM Parameters

    • Description: RSEM parameters. To set the CPU value, please use advanced tab and search for RSEM_Module_RSEM process settings.
    • Default value: ""

  • No BAM Output

    • Description: If true is selected, RSEM will not output any BAM file (default=false)
    • Available options: true (default), false

  • Output Genome BAM

    • Description: If true is selected, RSEM will generate a BAM file, with alignments mapped to genomic coordinates and annotated with their posterior probabilities. (default=true)
    • Available options: true (default), false

  • Sense/Antisense Quantification

    • Description: Quantify sense/antisense genes and transcripts
    • Available options: No (default), Yes

References & Resources

  • Tool Documentation: Contact the team for details on RSEM quantification methods
  • Related Papers: Li, B., & Dewey, C. N. (2011). RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC bioinformatics, 12(1), 323.